The Proteasix Ontology

Transcription

1 The Proteasix Ontology Mercedes Arguello Casteleiro 1, Julie Klein 2 and Robert Stevens 1 1 School of Computer Science, University of Manchester, Oxford road, Manchester, United Kingdom. 2 Institut National de la Sante et de la Recherche Médicale (INSERM), U1048, Toulouse, France. And Universite Toulouse III Paul-Sabatier, Toulouse, France.

2 Overview Biomedical background: Peptides as Biomarkers Current Tools & Applications DEMO 1 - Proteasix Web App Current limitations of Proteasix Web App Semantic Web technologies & Proteasix Ontology (PxO) Concluding remarks

3 Biomedical*Background* why omics? Omics: studying all molecules collectively Complex diseases cannot be adequately described by single features: - Interindividual differences - Mechanism multiplicity

4 Biomedical*Background* Exemplifying the challenges: CKD Renal biopsy (kidney status) Detect But too invasive Predict evolution Too late Albuminuria (glomerular filtration) Not always present Not sensitive enough egfr (glomerular filtration) Too late Too late New biomarkers: non-invasive, early changes, kidney status (To be used in addition/combination with gold-standards)

5 Pep2des*as*Biomarkers* Urinary peptides Peptide: proteolysis product (terminal post-translational modification) Mw (kda) Courtesy: C. Lacroix, Toulouse Proteins Peptides - Reduced pre-analytical handling before mass spectrometry analysis no digestion Improved resistance to degradation already degradation products - Peptides are filtered under physiological conditions detection of early events, before alteration of the filtration barrier

6 Links*of*urinary*pep2des*to* known*processes*in*ckd* Parent protein Protease Peptide

7 Links*of*urinary*pep2des*to* known*processes*in*ckd* Parent protein Protease Peptide Parent protein is associated to pathophysiology?

8 Links*of*urinary*pep2des*to* known*processes*in*ckd* Parent protein Protease Peptide Parent protein is associated to pathophysiology? And/or Protease activity is associated to pathophysiology?

9 Links*of*urinary*pep2des*to* known*processes*in*ckd* Parental*proteins* Filtration plasma proteins Serum)albumin) Apo9A1) Beta929microglobulin) Aberrant expression of ECM (Fibrosis) Inflammation Osteopon(n) Protein)S100)A9)) CD99) Tissue repair Clusterin) Annexin)A1) Collagen)alpha)I) Collagen)alpha)II) Collagen)alpha)III)

10 Links*of*urinary*pep2des*to* known*processes*in*ckd* Proteases* Protease identification: better understanding of disease mechanisms Acute renal allograft rejection Versus Stable graft Urine Clinical application Mass spectrometry Peptide biomarkers Mechanisms Collagen degradation: inflammatory cell infiltration AngII generation: macrophage recruitment Metzger, et al. Proteomics Clin Appl MMP8 IHC confirmation: Neutrophils surrounding capillaries Sequence information of identified altered collagen α(i) and α (III) chain fragments in rejection samples suggested an involvement of matrix metalloproteinase-8 (MMP-8).

11 Links*of*urinary*pep2des*to* known*processes*in*ckd* Proteases* Nomenclature: Cleavage site: 8 amino acid sequence (P4-P3-P2-P1 P1 -P2 -P3 -P4 ) Scissile bond: peptide bond between P1 and P1 Some proteases have very broad specificity (e.g. Trypsin X-X-X-R/K X-X-X-X) Some proteases have very strong specificity (e.g. Masp2 S-L-G-R K-I-Q-I) Some proteases have exopeptidase activity Some proteases have endopeptidase activity + +

12 Smith et al. Hypertension 2012 From*pep2des*to*enzymes?* Cathepsin*in*Diabe2c*nephropathy* In the large conduit arteries, elastin is important in maintaining vascular compliance. In predialysis chronic kidney disease (CKD), elastin degradation is an important determinant of arterial stiffness and is associated with all-cause mortality. Elastin degradation is mediated by several proteases, including matrix metalloproteinase 2 and cathepsin S. Higher matrix metalloproteinase 2 and elastinderived peptide levels were also independently associated with preexisting cardiovascular disease.

13 From*pep2des*to*enzymes?* Cathepsin*in*Diabe2c*nephropathy* Some math Proteasix) (Holger Husi Glasgow, UK) Top Predicted enzymes Cathepsin S Cathepsin V (L2) Urinary peptides in DN Cathepsin S Cathepsin V (L2) Known roles in extracellular matrix (ECM) degradation. Zero hour biopsy Cathepsin S increased in serum of CKD patients. Smith et al. Hypertension 2012 DN Unpublished (Gert Mayer, Innsbruck, Austria) Cathepsin V (L2)??

14 Tools*&*Applica2ons** Peptides represent a new source of very useful biomarkers in kidney and other disease. Peptides can help better understanding the pathophysiological mechanisms: Parental proteins Proteases

15 Tools*&*Applica2ons** Peptides represent a new source of very useful biomarkers in kidney and other disease. Peptides can help better understanding the pathophysiological mechanisms: Parental proteins Proteases HELP?

16 Tools*&*Applica2ons** Peptides can help better understanding the pathophysiological mechanisms* Let s get some HELP

17 Tools*&*Applica2ons** What)do)we)need?) P4-P3-P2-P1 P1 -P2 -P3 -P4 Nterm Peptide P4-P3-P2-P1 P1 -P2 -P3 -P4 Cterm 2 cleavage sites/peptides (N and C Term) Cleavage sites are incomplete! reconstruct full cleavage sites Identify proteases that can cleave these cleavage sites We need an automatic tool to reconstruct the cleavage sites We need to collect information about cleavage site/protease

18 Tools*&*Applica2ons** Exisiting tools for linking proteases, substrates, cleavage sites: CutDB (Proteolysis Map Project; PMAP) MEROPS TopFIND2 Proteasix

19 CutDB** Database of protease/cleavage site Not peptide-centric; No batch searches

20 MEROPS** Database of protease specificity Not peptide-centric; No batch searches

21 TopFIND2** Database Tool

22 Proteasix*WebNbased*version** Content:) Human proteases (230), mouse proteases (160), rat proteases (105) >20000 protease/cleavage site association (CutDB, MEROPS) 318 protease specifity matrices for prediction (MEROPS)

23 Proteasix*WebNbased*version** Content:) Human proteases (230), mouse proteases (160), rat proteases (105) >20000 protease/cleavage site association (CutDB, MEROPS) 318 protease specifity matrices for prediction (MEROPS) Func(onality:) Visualisation of protease specificity Cleavage site reconstruction (based on UniprotKB) Prediction of proteases

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25 Current*Limita2ons*of** Proteasix*Web*App** To refine the predictions, we need to know: " the species in which our proteins exist " the function of the protease " where the proteins live, i.e. which cellular component At the moment there is NO distinction between " Exopeptidase activity " Endopeptidase activity

26 Current*Limita2ons*of** Proteasix*Web*App** To refine the predictions, we need to know: " the species in which our proteins exist " the function of the protease " where the proteins live, i.e. which cellular component At the moment there is NO distinction between " Exopeptidase activity " Endopeptidase activity

27 Ontology* Challenge: how to go from information to Knowledge

28 Ontology* In informatics and computer science, an ontology is a representation of the shared background knowledge for a community.

29 Ontology* In informatics and computer science, an ontology is a representation of the shared background knowledge for a community.

30 The goal with a computer science ontology is to make knowledge of a domain computationally useful

31 The goal with a computer science ontology is to make knowledge of a domain computationally useful. An ontology is a description of the concepts and relationships that can exist Categories)or)classes:) Protein Gene Organism

32 The goal with a computer science ontology is to make knowledge of a domain computationally useful. An ontology is a description of the concepts and relationships that can exist Categories)or)classes:) Protein Gene Organism Rela(onships:) P02768 is-a protein ALB is-a gene P02768 only_in_taxon Human

33 Current*Work:* Proteasix Ontology (PxO) Concepts)

34 Current*Work:*Proteasix Ontology (PxO)

35 Current*Work:*Proteasix Ontology (PxO)

36 Proteasix Ontology (PxO) reuse*ontologies

37 Proteasix Ontology (PxO) reuse*ontologies chemical entity molecular entity Alanine

38 Proteasix Ontology (PxO) reuse*ontologies Human Rat Mouse

39 Proteasix Ontology (PxO) reuse*ontologies molecular_function cellular_component biological_process

40 Proteasix Ontology (PxO) reuse*ontologies Protein amino acid chain proteolytic cleavage product

41 The term Semantic Web refers to W3C s vision of the Web of linked data Ontologies are considered one of the pillars of the Semantic Web

42 Semantic Web technologies SWRL) (rules)) ) OWL9S) (services)) ) SPARQL) (queries)) OWL) (ontologies)) NEW) Proteasix)

43 Current*Work:*Proteasix Ontology (PxO) UniProt KB proteins (Swiss-prot and TrEMBL) " Organised by Taxons following PRO ontology " Annotated with GO biological_process; GO cellular_component; and GO molecular_function Model cleavage sites patterns for " Exopeptidase activity " Endopeptidase activity

44 For*using*Pep2des*as*Biomarkers,* we*need* more*data..*and*data*linkage..** Semantic Web technologies OWL) (ontologies)) Class: polypeptide_region SubClassOf: biological_region part_of some protein, associated_with some 'proteolytic cleavage product', only_in_taxon some organism

45 For*using*Pep2des*as*Biomarkers,** we*need* more*data..*and*data*linkage..** In Swiss-Prot there are proteins annotated with GO: , which is serine-type endopeptidase activity Semantic Web technologies SPARQL) (queries)) SELECT?x FROM <file:./ontofiles/swiss-prot.owl> {?x rdf:type owl:class; rdfs:subclassof [ a owl:restriction ; owl:onproperty pr:has_function ; owl:somevaluesfrom obo:go_ ]. }

46 For*using*Pep2des*as*Biomarkers,* we*need* more*data..*and*data*linkage..** Can we retrieve from Swiss-Prot ALL the proteins annotated with any DESCENDANT of Peptidase activity GO_ ? Semantic Web technologies SPARQL) (queries)) serine-type endopeptidase activity GO: GRAPH <file:./ontofiles/ GO_TAXONOMY_molecular_function.owl> {?C rdfs:subclassof+ obo:go_ }.

47 Can we retrieve from Swiss-Prot ALL the proteins annotated with any DESCENDANT of Peptidase activity GO_ ? Semantic Web technologies SPARQL) (queries)) For*using*Pep2des*as*Biomarkers,* we*need* more*data..*and*data*linkage..** SELECT?x FROM <file:./ontofiles/swiss-prot.owl)> FROM NAMED <file:./ontofiles/go_taxonomy_molecular_function.owl> { GRAPH <file:./ontofiles/go_taxonomy_molecular_function.owl> {?C rdfs:subclassof+ obo:go_ }. {?x rdf:type owl:class; rdfs:subclassof [ a owl:restriction ; owl:onproperty pr:has_function ; owl:somevaluesfrom?c ]. } }

48 Concluding*remarks* TopFIND2 and Proteasix can help to automatically predict modification of protease activity Current work: exploring the benefits of using Proteasix ontology (PxO) in the Semantic-Web version of Proteasix Hard Limits: Prediction always need validation Data available (over-representation of some proteases, other are missing)

49 ACKNOWLEDGMENT: to Julie Klein for providing " Biomedical background " Comparison of Current Tools & Applications